Chemical Evolution Theory of Life's Origins 1. the synthesis and accumulation of small organic molecules, or monomers, such as amino acids and nucleotides. • Production of glycine (an amino acid) energy 3HCN+2H2O −→ C2H5O2N+CN2H2. • Production of adenine (a base): 5 HCN → C5H5N5, • Production of ribose (a sugar): 5H2CO → C5H10O5. 2. the joining of these monomers into polymers, including proteins and nucleic acids. Bernal showed that clay-like materials could serve as sites for polymerization. 3. the concentration of these molecules into droplets, called protobionts, that had chemical characteristics different from their surroundings. This relies heavily on the formation of a semi-permeable membrane, one that allows only certain materials to flow one way or the other through it. Droplet formation requires a liquid with a large surface tension, such as water. Membrane formation naturally occurs if phospholipids are present. 4. The origin of heredity, or a means of relatively error-free reproduction. It is widely, but not universally, believed that RNA-like molecules were the first self-replicators — the RNA world hypothesis. They may have been preceded by inorganic self-replicators. Lattimer, AST 248, Lecture 13 – p.1/20 Acquisition of Organic Material and Water • In the standard model of the formatio of the solar system, volatile materials are concentrated in the outer solar system. Although there is as much carbon as nearly all other heavy elements combined in the Sun and the bulk of the solar nebula, the high temperatures in the inner solar system have lead to fractional amounts of C of 10−3 of the average. • Ices are similarly much more abundant in the outer solar system. • Meteorite and comet impacts could deliver much of the Earth’s volatile material, especially C and H2O. At present-day rates, a billion years is needed to deliver the C in Earth’s biosphere, but 4 billion years ago, the delivery rate was much larger. • Some simple organic materials would have been included in this delivered material, as indicated by their presence in the Murchison meteorite. • A reducing atmosphere on the early Earth would generate more organics. Lattimer, AST 248, Lecture 13 – p.2/20 Abiogenesis • Self-organization leads to more complex structure Big Bang → atoms → stars → galaxies • Crucial questions which did not have experimental answers up until now, but new evidence has become evident: • Synthesis of nucleotides • Polymerization of nucleotides • Incorporation of a self-copying gene into single cells upon which natural selection could act • “Gene-first” mechanism • “Metabolism-first” mechanism Primitive metabolism provides environment for later emergence of RNA replication. Example: Wächtershäuser’s iron-sulfur world theory, De Duve thioester theory. But can’t explain the high specificity of chemical reactions. Thermosynthesis world, involving thermal cycling, suggests an ATP-like enzyme that promotes peptide bonds: the “First Protein”. • Origin of homochirality • Genesis of the protein translation mechanism • Pieces are now coming together to support plausibility of spontaneous generation • Minimal number of genes seems to be about 206 in theory, in experiment there seem to be 387 essential genes • Evidence suggests that this complexity has evolved, step by step, from very simple beginnings Lattimer, AST 248, Lecture 13 – p.3/20 Monomer Production: • Step 1 is possible in the early Earth’s atmosphere if it was was highly reducing as opposed to oxidizing (cf. Miller & Urey experiment). Later research cast doubt on the existence of a reducing atmosphere and pointed to a neutral atmosphere dominated by CO2. More recent evidence is that H escaped very slowly on early Earth and its abundance wasn’t negligible after all. Supported by evidence from chondritic meteorites which were Earth’s building blocks. Discovery of highly reducing conditions near hydrothermal vents and in volcanos may make this debate irrelevant. • Energy sources to drive initial chemical reactions available from UV solar radiation, radioactivity, electrical discharges (lightning), cosmic rays and solar wind (Earth’s magnetic field not yet formed). Volcanic and vent energy available near hydrothermal vents. Lattimer, AST 248, Lecture 13 – p.4/20 The Role of Minerals Four key roles minerals could have played: • Protection and concentration Minerals acted as hosts, protecting them from dispersal and destruction. Example: volcanic rock containing many small air pockets formed from expanding gases; common minerals developing microscopic pits from weathering. • Support Surfaces act as support structures aiding accumulation and interaction. Example: clays. • Selection Many minerals have crystal faces that are mirror images. Calcite bonds strongly with amino acids, and left- and right-handed amino acids bond to different crystal faces. • Catalysis Nitrogen is important, but most of it is in the atmosphere as nonreactive N2. N2 and H2 passed over metal surfaces can bind and generate NH3, ammonia, a valuable source of nitrogen for biological reactions. Could have occurred near hydrothermal vents where iron oxide and iron sulfide surfaces are abundant. Lattimer, AST 248, Lecture 13 – p.5/20 Clays and Polymerization • Clay structure is that of alternating negatively charged sheets of Si O4 and Al O4 tetrahedra separated by positive cations (Ca, Na, Fe, or Mg). • Clays are extremely common on the Earth and Mars. • Charged layers and Andreas Trepte, translated by User:Itub; Wikipedia cations provide multitudinous sites for monomers to stick. • Water can easily flow through the structure as the layers are separted by 1 mm or more, enabling dehydration. • A cubic centimeter (thumb-tip) of clay has the net surface area of a football field. • Many peptide bonds are catalyzed by clays; RNA strands up to 100 bases in length have been produced in laboratories; lipids can be polymerized into pre-cells, sometimes containing short RNA strands. Lattimer, AST 248, Lecture 13 – p.6/20 Clays Lattimer, AST 248, Lecture 13 – p.7/20 Droplets and Boundary Layers How does self-assembly occur? • Certain materials are ambiphilic: they have a polar hydrophilic head and a hydrophobic tail. Hydrophilic materials can be dissolved in water. • Ambiphilic molecules added to water tend to stay on the surface with hydrophilic heads in the water, creating a single (or mono-) layer, i.e., a membrane. Formation of spheres, or micells, permits surface area and free energy reduction. In sufficient concentrations, ambiphilic molecules will form a double-layer structure, or bilayer. Spheres, or bilayer vesicles, will form. Lattimer, AST 248, Lecture 13 – p.8/20 Droplet Formation • High surface tension of water leads to large drops, not individual molecules Properties 8 small drops 1 large drop radius (mm) 1 2 volume per drop (mm3) (4π/3) · 13 (4π/3) · 23 total volume (mm3) 32π/3 32π/3 surface area per drop (mm2) 4π · 12 4π · 22 total surface area (mm2) 32π 16π • Polymeric clumps (coacervates) observed • Phospholipids self-assemble into films forming semi-permeable membranes • Concentration of polymers • Existence of enzymes for growth • Fission forms daughter drops • Limited raw material, growth enzyme • Random inheritance of important enzymes • Keys: Autocatalytic polymers, systematic inheritance www.daviddarling.info/imagesLattimer, AST 248, Lecture 13 – p.9/20 Droplet Formation organic molecules and membrane-bound bubbles primitive cells Lattimer, AST 248, Lecture 13 – p.10/20 Droplet Growth The droplet, consisting of protein and polysaccharide, contains the enzyme phosphorylase. Glucose-1-phosphate diffuses into the droplet and is polymerized to starch by the enzyme. The starch migrates to the wall, thickens it, and increases volume of droplet. The enzyme, phosphorylase, polymerizes glucose-1-phosphate to starch. A second enzyme, amylase, degrades the starch to maltose. Droplets containing both enzymes do not grow because the starch disappears as fast as it is made. Maltose diffuses back into surrounding medium. instruct1.cit.cornell.edu/courses/biog105/pages/demos/106/unit04/3a.protobionts.html Lattimer, AST 248, Lecture 13 – p.11/20 Why RNA Might Have Been First • RNA nucleotides are more easily synthesized than DNA nucleotides; • DNA’s greater stability argues it took over some of RNA’s roles; • RNA probably evolved before most proteins because no plausible scenario exists where proteins can replicate without RNA or DNA. • The molecule ATP is closely related to a monomer of RNA. This suggests a simpler RNA world existed once, in which RNA replicated and evolved without specialized proteins. Eventually, RNA became capable of transcribing DNA which is more efficient. RNA can create DNA, as is illustrated by the example of retroviruses. Natural selection led to the DNA + protein world which outcompeted the RNA world. Are retroviruses a dark legacy of our ancestors that can still wreak havoc in the modern world? Lattimer, AST 248, Lecture 13 – p.12/20 RNA World Hypothesis Prebiotic life has an RNA forerunner if it could: • replicate without proteins • catalyze all steps of protein synthesis RNA today does not have these properties. However • Proteins were not first, they can’t be catalyzed without gene information • DNA gene information without catalysis, provided by proteins, necessary for life’s functions, is useless Evidence for the “RNA World Hypothesis”: • New pathways recently found for nucleotide self-assembly • RNA, not protein, enzymes called ribozymes play a central role in protein synthesis, although proteins